X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=metastatscommand.h;h=82a2cd463fab9762b38bb26dabdef11a7e7a4a0a;hp=b4800b71d75bcda1bfa5a39db6f8191849d0b348;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/metastatscommand.h b/metastatscommand.h
index b4800b7..82a2cd4 100644
--- a/metastatscommand.h
+++ b/metastatscommand.h
@@ -25,7 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "metastats";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "White JR, Nagarajan N, Pop M (2009). Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352. \nhttp://www.mothur.org/wiki/Metastats"; }
 	string getDescription()		{ return "detects differentially abundant features in clinical metagenomic samples"; }
 
@@ -54,6 +56,9 @@ private:
 	
 	int process(vector<SharedRAbundVector*>&);
 	int driver(int, int, vector<SharedRAbundVector*>&);
+    int convertToShared(string filename);
+    int convertToInput(vector<SharedRAbundVector*>&, string);
+    bool convertSharedToInput;
 };
 
 /**************************************************************************************************/
@@ -66,7 +71,7 @@ struct metastatsData {
     vector<string> designMapGroups;
     vector<string> outputNames;
 	int start;
-	int num, iters;
+	int num, iters, count;
 	float threshold;
 	MothurOut* m;
 	string sharedfile;
@@ -84,6 +89,7 @@ struct metastatsData {
         designMapGroups = dg;
         iters = i;
         threshold = thr;
+        count=0;
 	}
 };
 /**************************************************************************************************/
@@ -97,7 +103,7 @@ static DWORD WINAPI MyMetastatsThreadFunction(LPVOID lpParam){
 		
         //for each combo
 		for (int c = pDataArray->start; c < (pDataArray->start+pDataArray->num); c++) {
-			
+			pDataArray->count++;
 			//get set names
 			string setA = pDataArray->namesOfGroupCombos[c][0]; 
 			string setB = pDataArray->namesOfGroupCombos[c][1];